Pointing Origins (POs) are positions defined in the focal plane of the telescope (in units of mm in the X, Y plane). The telescope software (i.e. MAGIQ) will place the target coordinates at this point in the focal plane. In addition, for appropriate tracking modes (i.e. vertical angle mode), this defines the point around which stars in the field will appear to rotate.
Most (all?) instruments have a REF pointing origin which places the target in a clear, easy to see position in the focal plane, so that the OAs can see the target (if it is bright enough of course) and perform any fine centering that is needed.
Once a target is centerred on REF, the OA would traditionally send it to a different pointing origin for science (e.g. SLIT). By simply selecting a new pointing origin, the target will move to the new position in the focal plane.